Contacts of the helix formed by residues 321 - 335 (chain B) in PDB entry 2Y01
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with PRO 321 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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318B ASP 4.4 1.3 - - - +
319B LEU 3.7 8.3 - - - +
320B VAL* 1.3 88.4 - - + +
322B ASP* 1.3 65.8 + - - +
323B TRP* 3.3 37.2 - - + +
324B LEU* 2.9 36.0 + - + +
325B PHE* 3.3 9.5 + - - +
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Residues in contact with ASP 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320B VAL 3.5 4.1 + - - -
321B PRO* 1.3 71.1 - - - +
323B TRP* 1.3 62.4 + - + +
325B PHE* 3.5 9.5 - - - +
326B VAL* 3.4 28.3 + - - +
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Residues in contact with TRP 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321B PRO* 3.3 32.3 - - + +
322B ASP* 1.3 80.4 - - + +
324B LEU* 1.3 94.4 + - + +
326B VAL* 3.5 8.1 + - - +
327B ALA* 2.9 31.9 + - + +
504B 2CV 5.7 3.9 - - + +
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Residues in contact with LEU 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309B VAL* 5.2 0.2 - - + -
320B VAL* 4.5 13.0 - - + -
321B PRO* 2.9 35.0 + - + +
323B TRP* 1.3 104.6 - - + +
325B PHE* 1.3 56.0 + - - +
327B ALA* 3.1 8.1 + - + +
328B PHE* 2.8 76.9 + - + +
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Residues in contact with PHE 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201B PHE* 5.1 21.3 - + + -
306B PHE* 3.6 32.2 - + - -
309B VAL* 3.4 35.4 - - + -
310B ASN* 4.1 19.7 - - - -
313B ASN* 3.7 26.0 - - - +
320B VAL* 4.3 5.6 - - + +
321B PRO 3.3 7.3 + - - +
322B ASP* 3.5 12.8 - - - +
324B LEU* 1.3 77.1 - - - +
326B VAL* 1.3 73.5 + - + +
328B PHE* 3.3 3.8 + - - +
329B ASN* 3.1 23.7 + - + +
601B Y00 5.2 10.1 - + + -
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Residues in contact with VAL 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B VAL* 5.3 1.6 - - + -
322B ASP* 3.4 21.7 + - - +
323B TRP* 3.8 9.6 - - - +
324B LEU 3.3 0.4 - - - -
325B PHE* 1.3 85.0 - - + +
327B ALA* 1.3 62.4 + - - +
329B ASN* 3.4 7.2 + - - +
330B TRP* 3.1 38.5 + - + +
504B 2CV 4.6 13.2 - - + -
601B Y00 3.9 38.1 - - + +
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Residues in contact with ALA 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323B TRP* 2.9 20.2 + - + +
324B LEU* 3.1 19.0 + - + +
326B VAL* 1.3 75.7 - - - +
328B PHE* 1.3 63.5 + - + +
330B TRP* 2.8 24.6 + - - +
331B LEU* 2.8 14.1 + - - +
504B 2CV 5.3 9.2 - - + +
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Residues in contact with PHE 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302B CYS 4.1 4.0 - - - +
305B PRO* 3.7 31.1 - - + +
306B PHE* 3.6 28.3 + - + +
309B VAL* 3.9 26.9 - - + -
324B LEU* 2.8 58.8 + - + +
325B PHE* 3.7 5.4 - - - +
327B ALA* 1.3 75.2 - - + +
329B ASN* 1.3 58.3 - - - +
331B LEU* 3.6 16.9 + - + +
332B GLY* 3.3 14.7 + - - -
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Residues in contact with ASN 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B ASP* 4.0 1.8 + - - -
303B TRP* 3.9 12.5 - - - -
306B PHE* 3.6 25.9 - - + -
325B PHE* 3.1 12.3 + - + +
326B VAL* 3.6 11.9 - - - +
327B ALA 3.1 0.6 - - - -
328B PHE* 1.3 75.6 - - - +
330B TRP* 1.3 61.0 + - - +
332B GLY* 3.3 2.6 + - - +
333B TYR* 3.1 49.7 + - - -
601B Y00 3.2 45.9 + - + +
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Residues in contact with TRP 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B MET* 3.1 39.0 - - + -
51B VAL* 4.9 5.2 - - + -
95B VAL* 3.9 20.4 - - + -
98B GLY* 3.8 24.2 - - - -
99B ALA 4.0 6.1 - - - -
102B VAL* 3.8 12.9 - - + +
326B VAL* 3.1 33.7 + - + -
327B ALA* 2.8 9.4 + - - +
329B ASN* 1.3 74.5 - - - +
331B LEU* 1.3 59.4 + - - +
332B GLY 3.1 1.3 - - - -
333B TYR* 3.1 38.8 + + + +
334B ALA* 2.8 28.6 + - - +
504B 2CV 3.6 45.7 + - + +
601B Y00 3.5 23.4 + + - -
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Residues in contact with LEU 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301B LEU 4.1 13.2 - - - +
302B CYS* 3.5 35.4 - - - +
305B PRO* 4.2 13.5 - - + -
327B ALA 2.8 11.3 + - - +
328B PHE* 3.6 22.2 - - + +
329B ASN 3.3 0.2 - - - -
330B TRP* 1.3 75.5 - - - +
332B GLY* 1.3 62.6 + - - +
334B ALA* 3.2 24.6 + - + +
335B ASN 3.4 4.7 + - - -
338B MET* 4.9 4.7 - - + -
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Residues in contact with GLY 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302B CYS* 3.5 7.7 + - - -
303B TRP* 3.4 44.8 + - - -
328B PHE 3.3 5.1 + - - -
329B ASN 3.3 7.2 + - - -
330B TRP 3.1 0.4 - - - -
331B LEU* 1.3 78.3 - - - +
333B TYR* 1.3 61.8 - - - +
335B ASN* 3.2 18.9 + - - +
336B SER* 4.3 2.3 + - - -
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Residues in contact with TYR 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B ILE* 4.1 8.1 - - - +
90B VAL* 4.2 10.4 - - + +
94B VAL* 3.6 25.8 - - + +
95B VAL* 3.9 20.4 - - + -
117B TRP* 3.8 6.8 - + - -
121B ASP* 2.8 35.6 + - - -
303B TRP* 4.2 7.0 - + - -
329B ASN* 3.1 28.5 + - - -
330B TRP* 3.1 49.6 + + + +
332B GLY* 1.3 75.5 - - - +
334B ALA* 1.3 63.6 + - - +
336B SER* 3.1 24.0 + - - -
601B Y00 3.4 30.5 - + - +
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Residues in contact with ALA 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B VAL* 5.8 5.2 - - - -
55B ILE* 5.5 2.0 - - - -
330B TRP 2.8 12.7 + - - +
331B LEU* 3.2 20.0 - - + +
332B GLY 3.1 0.2 - - - -
333B TYR* 1.3 77.5 - - - +
335B ASN* 1.3 59.8 + - - +
337B ALA* 3.1 23.8 + - - +
338B MET* 3.7 22.4 - - + +
504B 2CV 5.8 5.2 - - - +
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Residues in contact with ASN 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B ASP* 4.5 11.9 + - - +
128B SER* 5.7 0.6 + - - -
295B ILE 5.0 0.3 - - - +
298B VAL* 3.9 13.0 - - - +
299B PHE* 3.3 55.2 + - - +
302B CYS* 3.7 16.5 - - + -
303B TRP* 4.4 3.6 - - - +
331B LEU 3.4 2.2 + - - -
332B GLY 3.2 14.3 + - - +
333B TYR 3.1 1.0 - - - -
334B ALA* 1.3 77.7 - - - +
336B SER* 1.3 58.3 + - - +
337B ALA 3.0 5.3 + - - -
338B MET* 3.1 23.9 + - - +
339B ASN* 4.1 16.8 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il